Hi Zach
LICSS (https://github.com/KevinLawson/excel-cdk) tackles this problem by
using text manipulation of Smiles. This approach is made robust by using
the 'Dot Disconnect' trick, described in this context by the authors of
SMILIB: (Schüller, Andreas & Schneider, Gisbert & Byvatov, Evgeny. (2003).
SMILIB: rapid assembly of combinatorial libraries in SMILES notation. QSAR
& Combinatorial Science. 22. 719 - 721. 10.1002/qsar.200310008). Basically,
R groups are combined by denoting the connection points with the notation
used for ring junctions and using a '.' to concatenate the two fragments to
be joined. This creates legal SMILES for the enumerated molecules. In
LICSS, this SMILES is then checked and standardised by reading in each
enumerated SMILES string into CDK and re-outputing SMILES for the resulting
AtomContainer. The text manipulation of the SMILES is very fast and LICSS
accomplishes this with simple Visual Basic. If you are interested in the
VBA code for enumeration, install LICSS, then with the VBA window in Excel
open [Alt F11] look at the EnumerateWorkSheet subroutine (and the doRecEnum
function it calls) - both in the SSS module. If you don't have Excel then I
can send you the code as text which you could adapt and improve as
necessary...
Best wishes
Kevin
On Mon, Jan 8, 2018 at 4:53 PM, Zach Charlop-Powers <
[email protected]> wrote:
> Hi CDK-Users,
>
> I am wondering if anyone has a suggestion on the best way to
> combinatorially expand R groups.
>
> Lets say that I have three R groups and three possibilities for each
> group. What would be the best way to generate all 27 of the compounds? I
> can imagine it would be possible to use string replacement in SMILES but
> that seems a bit brittle. Is there a way to do PseudoAtom substitution
> with CDK itself? I'm asking here before poking around the API in the
> hopes that this is an easy problem that is already solved.
>
> Thanks,
> zach cp
>
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